This category is for sites about stand-alone computer programs which process biological information such as genetic sequences....
This page was last updated on August 24th, 2008
This page was last updated on August 24th, 2008
Software (from Bioinformatics)
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Linux Software Encyclopedia - Bioinformatics
Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
Premier Biosoft International
Developers of software for real time PCR primer design, TaqMan, molecular beacons, DNA microarray analysis, drawing restriction plasmid maps, gateway cloning experiments, protein interaction network and functional genomics.
AcaClone pDRAW32
Freeware DNA cloning, analysis and visualization software.
NCBI BLAST
BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
XDigitize
A visualization software system for evaluation of hybridisation experiments.
DNA-Star - Lasergene
Commercial sequence analysis and manipulation suite for Windows and Macintosh.
Gene Expression Data Analysis web application
Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation, and links to external genomic databases.
The FASTA package of sequence comparison programs
William Pearson's package for fast sequence comparison
WU-BLAST Archives
WU-BLAST: The Washington University BLAST. "...faster at any sensitivity, more sensitive at any speed, the first BLAST with gapped alignments and statistics."
ARCiB -- Accessible Retired Computers in Biology
NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.
GDE for Linux
An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.
BSML - Bioinformation Sequence Markup Language
Extensible language specification and container for bioinformatic data.
limmaGUI
A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
PubCrawler - An Update Alerting Service for PubMed and GenBank
Software and an online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
Software for Statistical Folding and Rational Design of Nucleic Acids
Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use.
Logical Depth
Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
JAligner
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
Computer Program for Polyphasic Taxonomy Analysis
The proBiosys suite of programs compares phenetic, chemotaxonomic and nucleic acid sequence data. Algorithms for polyphasic taxonomy are available to construct Dendrograms, the suite is simple to use.
AnnHyb - Nucleotidic Sequence Manager
Free software for working with and managing nucleotide sequences in multiple formats. Many features including sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.
Array Genetics
Bioinformatics programs, including MendelBase.
Verbumculus Genetic Sequence Analyzer
An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Executable for Sparc-Solaris, Sparc-Intel or Linux-Intel. Also available as a Java applet.
Artemis: A DNA Sequence Viewer and Annotation Tool
Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
AbOrygen : Intuitive bioinformatics
AbOrygen develops the next generation of bioinformatics software with powerful new features that simplify and improve the research work of life scientists worldwide.
The Sanger Centre: Software
Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
Phred/Phrap/Consed System Home Page
basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
GeneticXchange
Software for life science discovery; enterprise-level data integration and desktop biologists.
Sequence Analysis for Mac OS X
A freeware Mac OS X application written in Java that does many standard types of DNA and protein sequence analysis tasks.
Gints
Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
Metalifesocieties
Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
Meta-MEME v2.0.1
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
STRING
Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
PHRED - Base-Calling Software with Quality Information
A widely-used program for calling DNA sequence bases from sequencer trace files.
HMMER - profile hidden Markov models for sequence analysis
Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools
Bio Informatic Bacterial Identification
Bibliographic site for management and alignment of bacteria and fungi sequences.
LucID Professional
Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
GeneRunner for Windows
A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
The ARB Project
A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface
Molecular Evolutionary Genetics Analysis (MEGA2) software
Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
Sight
Extendable parallel system for automatic genome analysis. Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Features for converting between naming systems, s
DARWIN
An interactive tool for peptide and nucleotide sequence analysis
EMBOSS
The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprieatry systems like GCG.
Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
Developers of software for real time PCR primer design, TaqMan, molecular beacons, DNA microarray analysis, drawing restriction plasmid maps, gateway cloning experiments, protein interaction network and functional genomics.
Freeware DNA cloning, analysis and visualization software.
BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
A visualization software system for evaluation of hybridisation experiments.
Commercial sequence analysis and manipulation suite for Windows and Macintosh.
Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation, and links to external genomic databases.
William Pearson's package for fast sequence comparison
WU-BLAST: The Washington University BLAST. "...faster at any sensitivity, more sensitive at any speed, the first BLAST with gapped alignments and statistics."
NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.
An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.
Extensible language specification and container for bioinformatic data.
A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
Software and an online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use.
Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
The proBiosys suite of programs compares phenetic, chemotaxonomic and nucleic acid sequence data. Algorithms for polyphasic taxonomy are available to construct Dendrograms, the suite is simple to use.
Free software for working with and managing nucleotide sequences in multiple formats. Many features including sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.
Bioinformatics programs, including MendelBase.
An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Executable for Sparc-Solaris, Sparc-Intel or Linux-Intel. Also available as a Java applet.
Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
AbOrygen develops the next generation of bioinformatics software with powerful new features that simplify and improve the research work of life scientists worldwide.
Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
Software for life science discovery; enterprise-level data integration and desktop biologists.
A freeware Mac OS X application written in Java that does many standard types of DNA and protein sequence analysis tasks.
Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
A widely-used program for calling DNA sequence bases from sequencer trace files.
Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools
Bibliographic site for management and alignment of bacteria and fungi sequences.
Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface
Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
Extendable parallel system for automatic genome analysis. Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Features for converting between naming systems, s
An interactive tool for peptide and nucleotide sequence analysis
The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprieatry systems like GCG.
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